To identify and provide a global assessment of DNA methylation in fetal ventricular septal defect (VSD), genomic DNA extracted from fetal myocardial tissue samples with VSD (n=21) and from normal fetal myocardial tissue samples (n=15) was analyzed for gene methylation using array‑based technology. Furthermore, the KIAA0310, RAB43, SIVA1 and NDRG2 genes were randomly selected for validation analysis using methylation-specific PCR. Our results revealed that 70 and 85 genes were regulated by hypermethylation and hypomethylation, respectively, in VSD. Different clusters of genes were associated with functions including embryo development, signal transduction, cell apoptosis and cell proliferation. In conclusion, this study identified a set of candidate genes whose expression is regulated by DNA methylation in fetal VSD.